Supplemental Figure 2. Multiple alignment of complete primary MRSA blood isolate genomes.
A) Maximum likelihood phylogenetic tree based on core genome SNVs of all primary MRSA blood isolates from 132 MSH inpatients (left), with a graphical representation of the complete genome alignment (right). Core syntenic blocks found in all strains are indicated by solid rectangles and accessory (non-core) syntenic blocks absent from at least one strain are indicated by patterned rectangles. Core blocks are colored according to the block location in each genome to highlight inversions (legend at bottom). Regions between the core blocks consist of accessory blocks (patterned rectangles) or unique sequence (solid black lines). These regions are placed equidistant between core blocks if the non-core region is found adjacent to the core block on either side. If the non-core region cannot be placed in between the core blocks to which it is adjacent (i.e. due to a structure of the genome being different to the reference) the region is attached arbitrarily to one of the core blocks to which it is adjacent. (see key below). Asterisk: location of the putative ICE element shown in C. B) Representation of all accessory genome blocks greater than 500 bp. Blocks are colored based on whether they originated from prophage, SCCmec, plasmid, or other uncategorized elements. A color key is included at the bottom.